Win32::Exe has issues for a long time Bug #110605 for Win32-Exe: exe_update produces broken EXE file when ProductName/FileDescription is specified

Well, it should be quite easy to patch the console/windowed flag in the EXE file without Win32::Exe. Wikipedia has a nice overview image in Portable Executable, and Microsoft currently offers a detailed description in PE Format (Windows). The relevant field is located in the optional headers, section Windows-specific fields. Its name is simply "Subsystem" and should contain a value documented in Windows Subsystem. IMAGE_SUBSYSTEM_WINDOWS_GUI = 2 indicates a windowed application, IMAGE_SUBSYSTEM_WINDOWS_CUI = 3 indicates a console application. There are more valid values, including OS/2, POSIX subsystem, drivers, EFI and XBOX stuff.

Alexander